Title: Fast Matrix Operations via the Woodbury Matrix Identity
Description: A hierarchy of classes and methods for manipulating matrices formed implicitly from the sums of the inverses of other matrices, a situation commonly encountered in spatial statistics and related fields. Enables easy use of the Woodbury matrix identity and the matrix determinant lemma to allow computation (e.g., solving linear systems) without having to form the actual matrix. More information on the underlying linear algebra can be found in Harville, D. A. (1997) <doi:10.1007/b98818>.
Author: Michael Bertolacci [aut, cre, cph]
Maintainer: Michael Bertolacci <m.bertolacci@gmail.com>
Diff between WoodburyMatrix versions 0.0.1 dated 2020-08-10 and 0.0.2 dated 2022-09-12
DESCRIPTION | 7 MD5 | 14 - NEWS.md | 4 R/WoodburyMatrix.R | 2 build/vignette.rds |binary inst/doc/WoodburyMatrix.html | 398 ++++++++---------------------- tests/testthat/test-WoodburyMatrix.R | 4 tests/testthat/test-normal-distribution.R | 2 8 files changed, 126 insertions(+), 305 deletions(-)
More information about WoodburyMatrix at CRAN
Permanent link
Title: Play a Game of 2048 in the Console
Description: Generates a game of 2048 that can be played in the
console. Supports grids of arbitrary sizes, undoing the last move,
and resuming a game that was exited during the current session.
Author: Alexander Rossell Hayes [aut, cre, cph]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between twenty48 versions 0.2.0 dated 2021-04-24 and 0.2.1 dated 2022-09-12
DESCRIPTION | 8 +-- MD5 | 18 ++++---- NAMESPACE | 12 +++-- NEWS.md | 6 ++ R/Twenty48_class.R | 17 +++++--- R/play_2048.R | 21 ++++----- R/sysdata.rda |binary R/twenty48-package.R | 3 + README.md | 102 ++++++++++++++++++++++++------------------------ man/twenty48-package.Rd | 6 -- 10 files changed, 103 insertions(+), 90 deletions(-)
Title: Retrieve ESPN Fantasy Football Data
Description: Format the raw data from the ESPN fantasy football API
<https://fantasy.espn.com/apis/v3/games/ffl/> as data frames.
Retrieve data on public leagues, rosters, athletes, and matches.
Author: Kiernan Nicholls [aut, cre, cph]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>
Diff between fflr versions 2.0.3 dated 2022-04-06 and 2.1.0 dated 2022-09-12
DESCRIPTION | 8 MD5 | 46 +- NEWS.md | 5 R/api.R | 4 R/data.R | 20 - R/fflr.R | 2 R/live.R | 2 R/outlook.R | 2 R/players.R | 33 + R/scores.R | 4 README.md | 54 +- build/vignette.rds |binary data/nfl_players.rda |binary data/nfl_schedule.rda |binary data/nfl_teams.rda |binary inst/doc/fantasy-football.R | 4 inst/doc/fantasy-football.Rmd | 8 inst/doc/fantasy-football.html | 748 ++++++++++++++++++++++++++--------------- man/ffl_api.Rd | 4 man/fflr.Rd | 2 man/nfl_players.Rd | 8 man/nfl_schedule.Rd | 6 man/nfl_teams.Rd | 6 vignettes/fantasy-football.Rmd | 8 24 files changed, 612 insertions(+), 362 deletions(-)
Title: Load CPS Microdata into R Using the 'Census Bureau Data' API
Description: Load Current Population Survey (CPS) microdata into R using the
'Census Bureau Data' API
(<https://www.census.gov/data/developers/data-sets.html>), including basic
monthly CPS and CPS ASEC microdata.
Author: Matt Saenz [aut, cre]
Maintainer: Matt Saenz <mattsaenz165@gmail.com>
Diff between cpsR versions 0.5.0 dated 2022-02-09 and 0.6.0 dated 2022-09-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/get_data.R | 4 ++-- R/utils.R | 4 ++-- README.md | 3 +-- man/get_asec.Rd | 2 +- man/get_basic.Rd | 2 +- 8 files changed, 23 insertions(+), 19 deletions(-)
Title: Statistics for Matrix Distributions
Description: Tools for phase-type distributions including the following variants:
continuous, discrete, multivariate, in-homogeneous, right-censored, and regression.
Methods for functional evaluation, simulation and estimation using the
expectation-maximization (EM) algorithm are provided for all models.
The methods of this package are based on the following references.
Asmussen, S., Nerman, O., & Olsson, M. (1996) <https://www.jstor.org/stable/4616418>,
Olsson, M. (1996) <https://www.jstor.org/stable/4616419>,
Albrecher, H., & Bladt, M. (2019) <doi:10.1017/jpr.2019.60>,
Albrecher, H., Bladt, M., & Yslas, J. (2020) <doi:10.1111/sjos.12505>,
Albrecher, H., Bladt, M., Bladt, M., & Yslas, J. (2022) <doi:10.1016/j.insmatheco.2022.08.001>,
Bladt, M., & Yslas, J. (2022) <doi:10.1080/03461238.2022.2097019>,
Bladt, M. (2022) <doi:10.1017/asb.2021.40>,
Bladt, M. (2022). <arXiv:2110.05179>,
Albrecher, H., Bladt, M., & Mueller, A. (2022) [...truncated...]
Author: Martin Bladt [aut, cre],
Jorge Yslas [aut],
Alaric Mueller [ctb]
Maintainer: Martin Bladt <martinbladt@gmail.com>
Diff between matrixdist versions 1.1.3 dated 2021-09-03 and 1.1.4 dated 2022-09-12
matrixdist-1.1.3/matrixdist/man/LInf_norm.Rd |only matrixdist-1.1.3/matrixdist/man/cumulateMatrix.Rd |only matrixdist-1.1.3/matrixdist/man/cumulateVector.Rd |only matrixdist-1.1.3/matrixdist/man/derivativeMatrixweibull.Rd |only matrixdist-1.1.3/matrixdist/man/diagonal_vector.Rd |only matrixdist-1.1.3/matrixdist/man/embeddedMC.Rd |only matrixdist-1.1.3/matrixdist/man/initialState.Rd |only matrixdist-1.1.3/matrixdist/man/matrixExpSum_arma.Rd |only matrixdist-1.1.3/matrixdist/man/matrixMax.Rd |only matrixdist-1.1.3/matrixdist/man/matrixMaxDiagonal.Rd |only matrixdist-1.1.3/matrixdist/man/matrix_VanLoan.Rd |only matrixdist-1.1.3/matrixdist/man/matrix_VanLoanArma.Rd |only matrixdist-1.1.3/matrixdist/man/matrix_exponential_slow.Rd |only matrixdist-1.1.3/matrixdist/man/matrix_inverse_slow.Rd |only matrixdist-1.1.3/matrixdist/man/matrix_product_slow.Rd |only matrixdist-1.1.3/matrixdist/man/matrix_sum.Rd |only matrixdist-1.1.3/matrixdist/man/newState.Rd |only matrixdist-1.1.3/matrixdist/man/reversTransformData.Rd |only matrixdist-1.1.3/matrixdist/man/solve_linear_system.Rd |only matrixdist-1.1.3/matrixdist/man/sumPH.Rd |only matrixdist-1.1.3/matrixdist/man/vectorOfMatrices_arma.Rd |only matrixdist-1.1.3/matrixdist/man/vectorOfMatrices_arma2.Rd |only matrixdist-1.1.3/matrixdist/src/auxilliary.cpp |only matrixdist-1.1.3/matrixdist/src/auxilliary.h |only matrixdist-1.1.3/matrixdist/src/exp_arm.cpp |only matrixdist-1.1.3/matrixdist/src/exp_arm.h |only matrixdist-1.1.3/matrixdist/src/matrix_functions.h |only matrixdist-1.1.4/matrixdist/DESCRIPTION | 38 matrixdist-1.1.4/matrixdist/MD5 | 411 + matrixdist-1.1.4/matrixdist/NAMESPACE | 24 matrixdist-1.1.4/matrixdist/R/0.generics.R | 151 matrixdist-1.1.4/matrixdist/R/1.ph.R | 410 + matrixdist-1.1.4/matrixdist/R/2.iph.R | 167 matrixdist-1.1.4/matrixdist/R/2b.iph_regression.R | 177 matrixdist-1.1.4/matrixdist/R/3.mph.R |only matrixdist-1.1.4/matrixdist/R/3b.miph.R |only matrixdist-1.1.4/matrixdist/R/3b.miph.nnet.R |only matrixdist-1.1.4/matrixdist/R/4.MPHstar.R |only matrixdist-1.1.4/matrixdist/R/4b.bivph.R |only matrixdist-1.1.4/matrixdist/R/5.phMoE.R |only matrixdist-1.1.4/matrixdist/R/6.sph.R | 165 matrixdist-1.1.4/matrixdist/R/7.dph.R |only matrixdist-1.1.4/matrixdist/R/RcppExports.R | 2133 ++++++---- matrixdist-1.1.4/matrixdist/man/EM_step_mPH_rc.Rd |only matrixdist-1.1.4/matrixdist/man/EMstep_MoE_PADE.Rd |only matrixdist-1.1.4/matrixdist/man/EMstep_PADE.Rd | 18 matrixdist-1.1.4/matrixdist/man/EMstep_RK.Rd | 18 matrixdist-1.1.4/matrixdist/man/EMstep_UNI.Rd | 18 matrixdist-1.1.4/matrixdist/man/EMstep_bivph.Rd |only matrixdist-1.1.4/matrixdist/man/EMstep_dph.Rd |only matrixdist-1.1.4/matrixdist/man/EMstep_dph_MoE.Rd |only matrixdist-1.1.4/matrixdist/man/Fisher-sph-method.Rd | 10 matrixdist-1.1.4/matrixdist/man/Fisher.Rd | 6 matrixdist-1.1.4/matrixdist/man/LRT-ph-ph-method.Rd | 2 matrixdist-1.1.4/matrixdist/man/LRT.Rd | 11 matrixdist-1.1.4/matrixdist/man/MPHstar-class.Rd |only matrixdist-1.1.4/matrixdist/man/MPHstar.Rd |only matrixdist-1.1.4/matrixdist/man/MPHstar_EMstep_UNI.Rd |only matrixdist-1.1.4/matrixdist/man/MPHstar_data_aggregation.Rd |only matrixdist-1.1.4/matrixdist/man/MoE-dph-method.Rd |only matrixdist-1.1.4/matrixdist/man/MoE-ph-method.Rd |only matrixdist-1.1.4/matrixdist/man/MoE.Rd |only matrixdist-1.1.4/matrixdist/man/Q_null_null.Rd |only matrixdist-1.1.4/matrixdist/man/Q_null_pos.Rd |only matrixdist-1.1.4/matrixdist/man/Q_pos_null.Rd |only matrixdist-1.1.4/matrixdist/man/Q_pos_pos.Rd |only matrixdist-1.1.4/matrixdist/man/TVR-MPHstar-method.Rd |only matrixdist-1.1.4/matrixdist/man/TVR.Rd |only matrixdist-1.1.4/matrixdist/man/a_rungekutta.Rd | 12 matrixdist-1.1.4/matrixdist/man/bivph-class.Rd |only matrixdist-1.1.4/matrixdist/man/bivph.Rd |only matrixdist-1.1.4/matrixdist/man/bivph_density.Rd |only matrixdist-1.1.4/matrixdist/man/bivph_tail.Rd |only matrixdist-1.1.4/matrixdist/man/cdf-dph-method.Rd |only matrixdist-1.1.4/matrixdist/man/cdf-iph-method.Rd | 13 matrixdist-1.1.4/matrixdist/man/cdf-miph-method.Rd |only matrixdist-1.1.4/matrixdist/man/cdf-mph-method.Rd |only matrixdist-1.1.4/matrixdist/man/cdf-ph-method.Rd | 13 matrixdist-1.1.4/matrixdist/man/cdf.Rd | 6 matrixdist-1.1.4/matrixdist/man/clone_matrix.Rd | 5 matrixdist-1.1.4/matrixdist/man/clone_vector.Rd | 5 matrixdist-1.1.4/matrixdist/man/coef-bivph-method.Rd |only matrixdist-1.1.4/matrixdist/man/coef-dph-method.Rd |only matrixdist-1.1.4/matrixdist/man/coef-iph-method.Rd | 4 matrixdist-1.1.4/matrixdist/man/coef-ph-method.Rd | 2 matrixdist-1.1.4/matrixdist/man/coef-sph-method.Rd | 4 matrixdist-1.1.4/matrixdist/man/cumulate_matrix.Rd |only matrixdist-1.1.4/matrixdist/man/cumulate_vector.Rd |only matrixdist-1.1.4/matrixdist/man/default_step_length.Rd | 7 matrixdist-1.1.4/matrixdist/man/dens-bivph-method.Rd |only matrixdist-1.1.4/matrixdist/man/dens-dph-method.Rd |only matrixdist-1.1.4/matrixdist/man/dens-iph-method.Rd | 10 matrixdist-1.1.4/matrixdist/man/dens-miph-method.Rd |only matrixdist-1.1.4/matrixdist/man/dens-mph-method.Rd |only matrixdist-1.1.4/matrixdist/man/dens-ph-method.Rd | 10 matrixdist-1.1.4/matrixdist/man/dens.Rd | 6 matrixdist-1.1.4/matrixdist/man/dph-class.Rd |only matrixdist-1.1.4/matrixdist/man/dph.Rd |only matrixdist-1.1.4/matrixdist/man/dphcdf.Rd |only matrixdist-1.1.4/matrixdist/man/dphdensity.Rd |only matrixdist-1.1.4/matrixdist/man/embedded_mc.Rd |only matrixdist-1.1.4/matrixdist/man/evaluate-sph-method.Rd | 6 matrixdist-1.1.4/matrixdist/man/evaluate.Rd | 8 matrixdist-1.1.4/matrixdist/man/expm_terms.Rd |only matrixdist-1.1.4/matrixdist/man/expmat.Rd |only matrixdist-1.1.4/matrixdist/man/find_n.Rd |only matrixdist-1.1.4/matrixdist/man/find_weight.Rd |only matrixdist-1.1.4/matrixdist/man/fit-MPHstar-method.Rd |only matrixdist-1.1.4/matrixdist/man/fit-dph-method.Rd |only matrixdist-1.1.4/matrixdist/man/fit-mph-method.Rd |only matrixdist-1.1.4/matrixdist/man/fit-ph-method.Rd | 28 matrixdist-1.1.4/matrixdist/man/fit.Rd | 8 matrixdist-1.1.4/matrixdist/man/haz-ph-method.Rd | 10 matrixdist-1.1.4/matrixdist/man/haz.Rd | 6 matrixdist-1.1.4/matrixdist/man/inf_norm.Rd |only matrixdist-1.1.4/matrixdist/man/initial_state.Rd |only matrixdist-1.1.4/matrixdist/man/iph-class.Rd | 10 matrixdist-1.1.4/matrixdist/man/iph.Rd | 18 matrixdist-1.1.4/matrixdist/man/logLik-ph-method.Rd | 4 matrixdist-1.1.4/matrixdist/man/logLikelihoodDPH.Rd |only matrixdist-1.1.4/matrixdist/man/logLikelihoodDPH_MoE.Rd |only matrixdist-1.1.4/matrixdist/man/logLikelihoodMgev_PADE.Rd | 16 matrixdist-1.1.4/matrixdist/man/logLikelihoodMgev_RK.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMgev_UNI.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMgompertz_PADE.Rd | 18 matrixdist-1.1.4/matrixdist/man/logLikelihoodMgompertz_PADEs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMgompertz_RK.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMgompertz_RKs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMgompertz_UNI.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMgompertz_UNIs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMloglogistic_PADE.Rd | 18 matrixdist-1.1.4/matrixdist/man/logLikelihoodMloglogistic_PADEs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMloglogistic_RK.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMloglogistic_RKs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMloglogistic_UNI.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMloglogistic_UNIs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMlognormal_PADE.Rd | 18 matrixdist-1.1.4/matrixdist/man/logLikelihoodMlognormal_PADEs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMlognormal_RK.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMlognormal_RKs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMlognormal_UNI.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMlognormal_UNIs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMpareto_PADE.Rd | 18 matrixdist-1.1.4/matrixdist/man/logLikelihoodMpareto_PADEs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMpareto_RK.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMpareto_RKs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMpareto_UNI.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMpareto_UNIs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMweibull_PADE.Rd | 18 matrixdist-1.1.4/matrixdist/man/logLikelihoodMweibull_PADEs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMweibull_RK.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMweibull_RKs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodMweibull_UNI.Rd | 20 matrixdist-1.1.4/matrixdist/man/logLikelihoodMweibull_UNIs.Rd | 24 matrixdist-1.1.4/matrixdist/man/logLikelihoodPH_MoE.Rd |only matrixdist-1.1.4/matrixdist/man/logLikelihoodPH_PADE.Rd | 18 matrixdist-1.1.4/matrixdist/man/logLikelihoodPH_PADEs.Rd | 22 matrixdist-1.1.4/matrixdist/man/logLikelihoodPH_RK.Rd | 18 matrixdist-1.1.4/matrixdist/man/logLikelihoodPH_RKs.Rd | 22 matrixdist-1.1.4/matrixdist/man/logLikelihoodPH_UNI.Rd | 18 matrixdist-1.1.4/matrixdist/man/logLikelihoodPH_UNIs.Rd | 22 matrixdist-1.1.4/matrixdist/man/m_exp_sum.Rd |only matrixdist-1.1.4/matrixdist/man/marginal_expectation.Rd |only matrixdist-1.1.4/matrixdist/man/matrix_exponential.Rd | 11 matrixdist-1.1.4/matrixdist/man/matrix_inverse.Rd | 7 matrixdist-1.1.4/matrixdist/man/matrix_power.Rd | 7 matrixdist-1.1.4/matrixdist/man/matrix_product.Rd | 6 matrixdist-1.1.4/matrixdist/man/matrix_vanloan.Rd |only matrixdist-1.1.4/matrixdist/man/max_diagonal.Rd |only matrixdist-1.1.4/matrixdist/man/maximum-dph-dph-method.Rd |only matrixdist-1.1.4/matrixdist/man/maximum-iph-iph-method.Rd | 8 matrixdist-1.1.4/matrixdist/man/maximum-ph-ph-method.Rd | 12 matrixdist-1.1.4/matrixdist/man/maximum.Rd | 10 matrixdist-1.1.4/matrixdist/man/merge_matrices.Rd |only matrixdist-1.1.4/matrixdist/man/mgevcdf.Rd | 23 matrixdist-1.1.4/matrixdist/man/mgevden.Rd | 23 matrixdist-1.1.4/matrixdist/man/mgompertzcdf.Rd | 17 matrixdist-1.1.4/matrixdist/man/mgompertzden.Rd | 15 matrixdist-1.1.4/matrixdist/man/minimum-dph-dph-method.Rd |only matrixdist-1.1.4/matrixdist/man/minimum-iph-iph-method.Rd | 8 matrixdist-1.1.4/matrixdist/man/minimum-ph-ph-method.Rd | 8 matrixdist-1.1.4/matrixdist/man/minimum.Rd | 10 matrixdist-1.1.4/matrixdist/man/miph-class.Rd |only matrixdist-1.1.4/matrixdist/man/miph.Rd |only matrixdist-1.1.4/matrixdist/man/mloglogisticcdf.Rd | 17 matrixdist-1.1.4/matrixdist/man/mloglogisticden.Rd | 15 matrixdist-1.1.4/matrixdist/man/mlognormalcdf.Rd | 17 matrixdist-1.1.4/matrixdist/man/mlognormalden.Rd | 15 matrixdist-1.1.4/matrixdist/man/moment-bivph-method.Rd |only matrixdist-1.1.4/matrixdist/man/moment-dph-method.Rd |only matrixdist-1.1.4/matrixdist/man/moment-ph-method.Rd | 8 matrixdist-1.1.4/matrixdist/man/moment.Rd | 8 matrixdist-1.1.4/matrixdist/man/mparetocdf.Rd | 17 matrixdist-1.1.4/matrixdist/man/mparetoden.Rd | 15 matrixdist-1.1.4/matrixdist/man/mph-class.Rd |only matrixdist-1.1.4/matrixdist/man/mph.Rd |only matrixdist-1.1.4/matrixdist/man/mweibullcdf.Rd | 19 matrixdist-1.1.4/matrixdist/man/mweibullden.Rd | 15 matrixdist-1.1.4/matrixdist/man/n_null.Rd |only matrixdist-1.1.4/matrixdist/man/n_pos.Rd |only matrixdist-1.1.4/matrixdist/man/new_exit_vec.Rd |only matrixdist-1.1.4/matrixdist/man/new_pi.Rd |only matrixdist-1.1.4/matrixdist/man/new_state.Rd |only matrixdist-1.1.4/matrixdist/man/new_subint_mat.Rd |only matrixdist-1.1.4/matrixdist/man/new_trans_exit.Rd |only matrixdist-1.1.4/matrixdist/man/new_trans_mat.Rd |only matrixdist-1.1.4/matrixdist/man/nnet_fit-mph-method.Rd |only matrixdist-1.1.4/matrixdist/man/nnet_fit.Rd |only matrixdist-1.1.4/matrixdist/man/null_states.Rd |only matrixdist-1.1.4/matrixdist/man/ph-class.Rd | 10 matrixdist-1.1.4/matrixdist/man/ph.Rd | 14 matrixdist-1.1.4/matrixdist/man/phcdf.Rd | 15 matrixdist-1.1.4/matrixdist/man/phdensity.Rd | 11 matrixdist-1.1.4/matrixdist/man/pi_null.Rd |only matrixdist-1.1.4/matrixdist/man/pi_pos.Rd |only matrixdist-1.1.4/matrixdist/man/plus-dph-dph-method.Rd |only matrixdist-1.1.4/matrixdist/man/plus-ph-ph-method.Rd | 8 matrixdist-1.1.4/matrixdist/man/plus_states.Rd |only matrixdist-1.1.4/matrixdist/man/pow2_matrix.Rd |only matrixdist-1.1.4/matrixdist/man/q_null.Rd |only matrixdist-1.1.4/matrixdist/man/q_pos.Rd |only matrixdist-1.1.4/matrixdist/man/quan-ph-method.Rd | 10 matrixdist-1.1.4/matrixdist/man/quan.Rd | 6 matrixdist-1.1.4/matrixdist/man/rMPHstar.Rd |only matrixdist-1.1.4/matrixdist/man/random_reward.Rd |only matrixdist-1.1.4/matrixdist/man/random_structure.Rd | 12 matrixdist-1.1.4/matrixdist/man/random_structure_bivph.Rd |only matrixdist-1.1.4/matrixdist/man/rdphasetype.Rd |only matrixdist-1.1.4/matrixdist/man/reg-ph-method.Rd | 28 matrixdist-1.1.4/matrixdist/man/reg.Rd | 8 matrixdist-1.1.4/matrixdist/man/revers_data_trans.Rd |only matrixdist-1.1.4/matrixdist/man/rew_sanity_check.Rd |only matrixdist-1.1.4/matrixdist/man/riph.Rd | 15 matrixdist-1.1.4/matrixdist/man/rmatrixgev.Rd | 17 matrixdist-1.1.4/matrixdist/man/rphasetype.Rd | 13 matrixdist-1.1.4/matrixdist/man/runge_kutta.Rd | 20 matrixdist-1.1.4/matrixdist/man/show-MPHstar-method.Rd |only matrixdist-1.1.4/matrixdist/man/show-bivph-method.Rd |only matrixdist-1.1.4/matrixdist/man/show-dph-method.Rd |only matrixdist-1.1.4/matrixdist/man/show-iph-method.Rd | 6 matrixdist-1.1.4/matrixdist/man/show-miph-method.Rd |only matrixdist-1.1.4/matrixdist/man/show-mph-method.Rd |only matrixdist-1.1.4/matrixdist/man/show-ph-method.Rd | 6 matrixdist-1.1.4/matrixdist/man/show-sph-method.Rd | 6 matrixdist-1.1.4/matrixdist/man/sim-MPHstar-method.Rd |only matrixdist-1.1.4/matrixdist/man/sim-bivph-method.Rd |only matrixdist-1.1.4/matrixdist/man/sim-dph-method.Rd |only matrixdist-1.1.4/matrixdist/man/sim-iph-method.Rd | 11 matrixdist-1.1.4/matrixdist/man/sim-miph-method.Rd |only matrixdist-1.1.4/matrixdist/man/sim-mph-method.Rd |only matrixdist-1.1.4/matrixdist/man/sim-ph-method.Rd | 8 matrixdist-1.1.4/matrixdist/man/sim.Rd | 6 matrixdist-1.1.4/matrixdist/man/sph-class.Rd | 6 matrixdist-1.1.4/matrixdist/man/sph.Rd | 8 matrixdist-1.1.4/matrixdist/man/sum_dph.Rd |only matrixdist-1.1.4/matrixdist/man/sum_ph.Rd |only matrixdist-1.1.4/matrixdist/man/transf_via_rew.Rd |only matrixdist-1.1.4/matrixdist/man/vector_of_matrices.Rd |only matrixdist-1.1.4/matrixdist/man/vector_of_matrices_2.Rd |only matrixdist-1.1.4/matrixdist/man/vector_of_powers.Rd |only matrixdist-1.1.4/matrixdist/src/EM_LL.cpp | 1123 ++--- matrixdist-1.1.4/matrixdist/src/EM_LL_PADE.cpp | 1435 ++++-- matrixdist-1.1.4/matrixdist/src/EM_LL_UNI.cpp | 983 ++-- matrixdist-1.1.4/matrixdist/src/EM_LL_UNI.h |only matrixdist-1.1.4/matrixdist/src/MPHstar_EMstep_UNI.cpp |only matrixdist-1.1.4/matrixdist/src/RcppExports.cpp | 1331 ++++-- matrixdist-1.1.4/matrixdist/src/Simulation.cpp | 339 - matrixdist-1.1.4/matrixdist/src/Simulation.h |only matrixdist-1.1.4/matrixdist/src/TVR.cpp |only matrixdist-1.1.4/matrixdist/src/TVR.h |only matrixdist-1.1.4/matrixdist/src/auxiliary.cpp |only matrixdist-1.1.4/matrixdist/src/distributions.cpp | 675 +-- matrixdist-1.1.4/matrixdist/src/distributions.h | 31 matrixdist-1.1.4/matrixdist/src/dph_EM_LL.cpp |only matrixdist-1.1.4/matrixdist/src/mPH_EM_UNI.cpp |only matrixdist-1.1.4/matrixdist/src/m_exp.cpp |only matrixdist-1.1.4/matrixdist/src/m_exp.h |only matrixdist-1.1.4/matrixdist/src/matrix_functions.cpp | 359 - matrixdist-1.1.4/matrixdist/src/operations.cpp | 92 matrixdist-1.1.4/matrixdist/src/structure_parameters.cpp | 119 280 files changed, 6733 insertions(+), 5089 deletions(-)
Title: 1970s BASIC Interpreter
Description: Executes BASIC programs from the 1970s, for historical and
educational purposes. This enables famous examples of early machine
learning, artificial intelligence, natural language processing, cellular
automata, and so on, to be run in their original form.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>
Diff between brassica versions 1.0.0 dated 2022-08-13 and 1.0.1 dated 2022-09-12
DESCRIPTION | 8 +-- MD5 | 43 +++++++++--------- NEWS |only R/brassica_enact.R | 44 +++++++++++++++--- R/brassica_eval.R | 96 +++++++++++++++++++++++++++++++++-------- R/brassica_prog.R | 21 +++++++- R/brassica_utils.R | 3 - inst/BASIC/animal.bas |only inst/BASIC/camel.bas | 4 - inst/BASIC/chase.bas | 2 inst/BASIC/eliza.bas | 2 inst/BASIC/flip.bas | 2 inst/BASIC/hammurabi.bas |only inst/BASIC/inkblot.bas | 2 inst/BASIC/life.bas | 13 +++-- inst/BASIC/maze.bas | 2 inst/BASIC/seabattle.bas | 2 inst/BASIC/super_star_trek.bas | 2 inst/BASIC/wumpus.bas | 2 inst/doc/BASIC.Rnw | 78 ++++++++++++++++++++++++++------- inst/doc/BASIC.pdf |binary man/NotRun.Rd | 30 ++++++++---- man/RUN.Rd | 4 + vignettes/BASIC.Rnw | 78 ++++++++++++++++++++++++++------- 24 files changed, 323 insertions(+), 115 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.32 dated 2022-08-10 and 0.33 dated 2022-09-12
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/paths.R | 29 ++++++++++++++++++++--------- R/revcheck.R | 2 +- R/utils.R | 4 ++++ inst/doc/xfun.html | 19 +++++++++++++------ man/file_ext.Rd | 16 +++++++++++++--- tests/test-cran/test-paths.R | 4 +++- 9 files changed, 71 insertions(+), 31 deletions(-)
Title: A Wrapper of the JavaScript Library 'DataTables'
Description: Data objects in R can be rendered as HTML tables using the
JavaScript library 'DataTables' (typically via R Markdown or Shiny). The
'DataTables' library has been included in this R package. The package name
'DT' is an abbreviation of 'DataTables'.
Author: Yihui Xie [aut, cre],
Joe Cheng [aut],
Xianying Tan [aut],
JJ Allaire [ctb],
Maximilian Girlich [ctb],
Greg Freedman Ellis [ctb],
Johannes Rauh [ctb],
SpryMedia Limited [ctb, cph] ,
Brian Reavis [ctb, cph] ,
Leon Gersen [ctb, cph] ,
Bartek Szopka [ct [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between DT versions 0.24 dated 2022-08-09 and 0.25 dated 2022-09-12
DESCRIPTION | 11 ++-- MD5 | 14 ++--- R/shiny.R | 25 +++++++--- inst/doc/DT.html | 21 +++++--- inst/htmlwidgets/lib/datatables-extensions/Buttons/js/jszip.min.js | 13 ++--- man/dataTableAjax.Rd | 13 ++++- man/dataTableOutput.Rd | 6 ++ tests/testit/test-datatables.R | 7 ++ 8 files changed, 78 insertions(+), 32 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks <doi:10.18637/jss.v098.i08>.
Author: Matteo Magnani [aut, cre],
Luca Rossi [aut] ,
Davide Vega [aut] ,
Obaida Hanteer [ctb]
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 4.0.1 dated 2022-01-04 and 4.1 dated 2022-09-12
DESCRIPTION | 10 MD5 | 76 +-- NEWS | 11 R/igraph.R | 40 +- man/Attributes.Rd | 14 man/Properties.Rd | 12 src/Makevars | 4 src/Makevars.win | 4 src/infomap/infomap/InfomapGreedyCommon.h | 1 src/infomap/infomap/MemNetwork.cpp | 1 src/infomap/infomap/MultiplexNetwork.cpp | 1 src/infomap/infomap/Network.h | 1 src/infomap/io/BipartiteClusterReader.cpp | 1 src/infomap/io/BipartiteClusterReader.h | 1 src/infomap/io/ClusterReader.h | 1 src/infomap/io/Config.h | 2 src/infomap/io/ProgramInterface.h | 4 src/infomap/io/version.cpp | 2 src/r_functions.cpp | 469 ++++++++---------------- src/r_functions.h | 6 src/rcpp_module_definition.cpp | 10 src/rcpp_utils.cpp | 24 - src/src/CMakeLists.txt | 13 src/src/community/community_stats.ipp | 4 src/src/community/mlp.hpp | 137 ++++--- src/src/community/modularity.hpp | 21 + src/src/community/modularity.ipp | 67 +++ src/src/core/stores/_impl/AttributeValueMap.ipp | 13 src/src/core/utils/CSVReader.cpp | 26 + src/src/core/utils/string.cpp | 1 src/src/io/_impl/read_common.cpp | 50 ++ src/src/io/_impl/read_common.hpp | 44 -- src/src/io/_impl/read_ml_common.hpp | 6 src/src/io/read_multilayer_network.cpp | 105 +++++ src/src/io/read_multilayer_network.hpp | 3 src/src/io/read_network.cpp | 49 -- src/src/io/read_network.hpp | 3 src/src/operations/project.ipp | 6 src/src/operations/sample.cpp |only src/src/operations/sample.hpp |only 40 files changed, 674 insertions(+), 569 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] ,
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] ,
Aust Frederik [ctb] ,
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Christophe Dervieux [ctb],
Clift [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.28 dated 2022-08-09 and 0.29 dated 2022-09-12
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/bs4_book.R | 4 +++- R/gitbook.R | 28 +++++++++++++++++++--------- man/gitbook.Rd | 14 ++++++-------- 5 files changed, 35 insertions(+), 25 deletions(-)
Title: Weighted and Directed Networks
Description: Implementations of network analysis including
(1) assortativity coefficient of weighted and directed networks,
Yuan, Yan and Zhang (2021) <doi:10.1093/comnet/cnab017>,
(2) centrality measures for weighted and directed networks,
Opsahl, Agneessens and Skvoretz (2010) <doi:10.1016/j.socnet.2010.03.006>,
Zhang, Wang and Yan (2022) <doi:10.1016/j.physa.2021.126438>,
(3) clustering coefficient of weighted and directed networks,
Fagiolo (2007) <doi:10.1103/PhysRevE.76.026107> and
Clemente and Grassi (2018) <doi:10.1016/j.chaos.2017.12.007>,
(4) network rewiring,
(5) preferential attachment network generation.
Author: Yelie Yuan [aut, cre],
Tiandong Wang [aut],
Jun Yan [aut],
Panpan Zhang [aut]
Maintainer: Yelie Yuan <yelie.yuan@uconn.edu>
Diff between wdnet versions 0.0.4 dated 2022-06-27 and 0.0.5 dated 2022-09-12
wdnet-0.0.4/wdnet/R/panet_control.R |only wdnet-0.0.5/wdnet/DESCRIPTION | 12 wdnet-0.0.5/wdnet/MD5 | 66 - wdnet-0.0.5/wdnet/NAMESPACE | 2 wdnet-0.0.5/wdnet/NEWS.md | 15 wdnet-0.0.5/wdnet/R/RcppExports.R | 86 ++ wdnet-0.0.5/wdnet/R/compile_pref.R |only wdnet-0.0.5/wdnet/R/joint_dist.R | 79 - wdnet-0.0.5/wdnet/R/rewire.R | 40 wdnet-0.0.5/wdnet/R/rpactl.R |only wdnet-0.0.5/wdnet/R/rpanet.R | 25 wdnet-0.0.5/wdnet/R/rpanet_general.R | 233 ++--- wdnet-0.0.5/wdnet/man/compile_pref_func.Rd |only wdnet-0.0.5/wdnet/man/dprewire.Rd | 7 wdnet-0.0.5/wdnet/man/dprewire.range.Rd | 8 wdnet-0.0.5/wdnet/man/dprewire_directed.Rd | 2 wdnet-0.0.5/wdnet/man/dprewire_undirected.Rd | 2 wdnet-0.0.5/wdnet/man/plus-.rpactl.Rd | 9 wdnet-0.0.5/wdnet/man/rpactl.edgeweight.Rd | 6 wdnet-0.0.5/wdnet/man/rpactl.newedge.Rd | 6 wdnet-0.0.5/wdnet/man/rpactl.preference.Rd | 107 ++ wdnet-0.0.5/wdnet/man/rpactl.reciprocal.Rd | 6 wdnet-0.0.5/wdnet/man/rpactl.scenario.Rd | 6 wdnet-0.0.5/wdnet/man/rpanet_binary_directed.Rd |only wdnet-0.0.5/wdnet/man/rpanet_binary_undirected_cpp.Rd |only wdnet-0.0.5/wdnet/man/rpanet_naive_directed_cpp.Rd |only wdnet-0.0.5/wdnet/man/rpanet_naive_undirected_cpp.Rd |only wdnet-0.0.5/wdnet/man/rpanet_nodelist_cpp.Rd | 4 wdnet-0.0.5/wdnet/src/RcppExports.cpp | 92 ++ wdnet-0.0.5/wdnet/src/funcPtrD.h |only wdnet-0.0.5/wdnet/src/funcPtrUnd.h |only wdnet-0.0.5/wdnet/src/init.c | 40 wdnet-0.0.5/wdnet/src/rpanet_binary_directed.cpp | 726 ++++++++---------- wdnet-0.0.5/wdnet/src/rpanet_binary_undirected.cpp | 425 +++++----- wdnet-0.0.5/wdnet/src/rpanet_naive_directed.cpp | 715 +++++++++-------- wdnet-0.0.5/wdnet/src/rpanet_naive_undirected.cpp | 449 ++++++----- wdnet-0.0.5/wdnet/src/rpanet_nodelist.cpp | 2 wdnet-0.0.5/wdnet/src/utils.cpp | 2 wdnet-0.0.5/wdnet/tests |only 39 files changed, 1809 insertions(+), 1363 deletions(-)
Title: Tools for HLA Data
Description: A streamlined tool for eplet analysis of donor and recipient HLA (human leukocyte antigen) mismatch. Messy, low-resolution HLA typing data is cleaned, and imputed to high-resolution using the NMDP (National Marrow Donor Program) haplotype reference database <https://haplostats.org/haplostats>. High resolution data is analyzed for overall or single antigen eplet mismatch using a reference table (currently supporting 'HLAMatchMaker' <http://www.epitopes.net> versions 2 and 3). Data can enter or exit the workflow at different points depending on the user's aims and initial data quality.
Author: Joan Zhang [aut, cre],
Aileen Johnson [aut],
Christian P Larsen [cph, aut]
Maintainer: Joan Zhang <joan.zhang@emory.edu>
Diff between hlaR versions 0.1.3 dated 2022-05-13 and 0.1.4 dated 2022-09-12
DESCRIPTION | 13 ++++++------- MD5 | 6 +++--- inst/doc/allele-haplotype.html | 25 +++++++++++++++++++------ inst/doc/eplet-mm.html | 13 ++++++++++--- 4 files changed, 38 insertions(+), 19 deletions(-)
Title: Linear Model Evaluation with Randomized Residuals in a
Permutation Procedure
Description: Linear model calculations are made for many random versions of data.
Using residual randomization in a permutation procedure, sums of squares are
calculated over many permutations to generate empirical probability distributions
for evaluating model effects. This packaged is described by
Collyer & Adams (2018). Additionally, coefficients, statistics, fitted values, and residuals generated over many
permutations can be used for various procedures including pairwise tests, prediction, classification, and
model comparison. This package should provide most tools one could need for the analysis of
high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Author: Michael Collyer [aut, cre] ,
Dean Adams [aut]
Maintainer: Michael Collyer <mlcollyer@gmail.com>
Diff between RRPP versions 1.3.0 dated 2022-06-21 and 1.3.1 dated 2022-09-12
DESCRIPTION | 6 +- MD5 | 20 ++++---- NEWS.md | 11 ++++ R/RRPP.utils.r | 94 ++++++++++++++++++++++++++++++++++++------ R/ordinate.r | 18 +++++++- build/vignette.rds |binary inst/doc/ANOVA.vs.MANOVA.html | 4 - inst/doc/Using.RRPP.html | 4 - man/ordinate.Rd | 16 +++++++ man/plot.lm.rrpp.Rd | 42 ++++++++++++++++++ man/plot.ordinate.Rd | 8 +++ 11 files changed, 191 insertions(+), 32 deletions(-)
Title: O-Stats, or Pairwise Community-Level Niche Overlap Statistics
Description: O-statistics, or overlap statistics, measure the degree of community-level trait overlap.
They are estimated by fitting nonparametric kernel density functions to each species’ trait
distribution and calculating their areas of overlap. For instance, the median pairwise overlap
for a community is calculated by first determining the overlap of each species pair
in trait space, and then taking the median overlap of each species pair in a community.
This median overlap value is called the O-statistic (O for overlap).
The Ostats() function calculates separate univariate overlap statistics for each trait,
while the Ostats_multivariate() function calculates a single multivariate overlap statistic for all traits.
O-statistics can be evaluated against null models to obtain standardized effect sizes.
'Ostats' is part of the collaborative Macrosystems Biodiversity Project "Local- to continental-scale
drivers of biodiversity across the National Ecological Observatory Network (NEON)."
For more infor [...truncated...]
Author: Quentin D. Read [aut, cre],
Arya Yue [aut],
Isadora E. Fluck [aut],
Benjamin Baiser [aut],
John M. Grady [aut],
Phoebe L. Zarnetske [aut],
Sydne Record [aut]
Maintainer: Quentin D. Read <quentin.read@usda.gov>
Diff between Ostats versions 0.1.1 dated 2021-11-16 and 0.2.0 dated 2022-09-12
DESCRIPTION | 6 MD5 | 30 + R/Ostats_multivariate.R | 2 R/Ostats_multivariate_plot.R | 2 R/Ostats_plot.R | 190 ++++++++++-- R/globals.R | 2 README.md | 1 build/vignette.rds |binary inst/doc/Ostats-introduction.html | 456 +++++++++++++++++++++++++----- inst/doc/Ostats-multivariate.html | 234 +++++++++++++-- man/Ostats_multivariate.Rd | 2 man/Ostats_plot.Rd | 50 ++- tests/testthat/Rplots.pdf |only tests/testthat/test-Ostats.R | 72 ++-- tests/testthat/test-Ostats_multivariate.R | 21 - tests/testthat/test-Ostats_plot.R |only tests/testthat/test-community_overlap.R | 11 17 files changed, 859 insertions(+), 220 deletions(-)
Title: Mixed Effects Cox Models
Description: Fit Cox proportional hazards models containing both
fixed and random effects. The random effects can have a general form, of which
familial interactions (a "kinship" matrix) is a particular special case.
Note that the simplest case of a mixed effects Cox model, i.e. a single random
per-group intercept, is also called a "frailty" model. The approach is based
on Ripatti and Palmgren, Biometrics 2002.
Author: Terry M. Therneau [aut, cre]
Maintainer: Terry M. Therneau <therneau.terry@mayo.edu>
Diff between coxme versions 2.2-17 dated 2022-06-03 and 2.2-18 dated 2022-09-12
coxme-2.2-17/coxme/tests/bdstest.R |only coxme-2.2-17/coxme/tests/bdstest.Rout.save |only coxme-2.2-18/coxme/DESCRIPTION | 6 +++--- coxme-2.2-18/coxme/MD5 | 26 ++++++++++++-------------- coxme-2.2-18/coxme/inst/NEWS.Rd | 6 ++++++ coxme-2.2-18/coxme/inst/doc/coxme.pdf |binary coxme-2.2-18/coxme/inst/doc/laplace.pdf |binary coxme-2.2-18/coxme/inst/doc/lmekin.R | 4 ++-- coxme-2.2-18/coxme/inst/doc/lmekin.Rnw | 4 ++-- coxme-2.2-18/coxme/inst/doc/lmekin.pdf |binary coxme-2.2-18/coxme/inst/doc/variance.R | 2 +- coxme-2.2-18/coxme/inst/doc/variance.Rnw | 2 +- coxme-2.2-18/coxme/inst/doc/variance.pdf |binary coxme-2.2-18/coxme/vignettes/lmekin.Rnw | 4 ++-- coxme-2.2-18/coxme/vignettes/variance.Rnw | 2 +- 15 files changed, 30 insertions(+), 26 deletions(-)
Title: Performing Bayesian Inference for Repeated-Measures Designs
Description: A Bayesian credible interval is interpreted with respect to posterior probability,
and this interpretation is far more intuitive than that of a frequentist confidence interval.
However, standard highest-density intervals can be wide due to between-subjects variability and tends
to hide within-subjects effects, rendering its relationship with the Bayes factor less clear
in within-subjects (repeated-measures) designs.
This urgent issue can be addressed by using within-subjects intervals in within-subjects designs,
which integrate four methods including the Loftus-Masson (1994) <doi:10.3758/BF03210951>,
the Rouder-Morey-Speckman-Province (2012) <doi:10.1016/j.jmp.2012.08.001>,
the Nathoo-Kilshaw-Masson (2018) <doi:10.1016/j.jmp.2018.07.005>,
and the Heck (2019) <doi:10.31234/osf.io/whp8t> interval estimates.
Author: Zhengxiao Wei [aut, cre] ,
Farouk S. Nathoo [aut] ,
Michael E.J. Masson [aut]
Maintainer: Zhengxiao Wei <zhengxiao@uvic.ca>
Diff between rmBayes versions 0.1.13 dated 2021-09-15 and 0.1.14 dated 2022-09-12
DESCRIPTION | 27 +++--- MD5 | 42 +++++----- NAMESPACE | 5 + R/rmBayes-package.R | 4 R/rmHDI.R | 18 ++-- R/stanmodels.R | 2 README.md | 146 ++++++++++++++++++----------------- man/rmHDI.Rd | 18 ++-- src/Makevars | 3 src/Makevars.win | 3 src/stanExports_HDIc.cc | 2 src/stanExports_HDIcCauchy.cc | 2 src/stanExports_HDIcUnif.cc | 2 src/stanExports_HDId.cc | 2 src/stanExports_HDIdCauchy.cc | 2 src/stanExports_HDIdCauchyFixed.cc | 2 src/stanExports_HDIdFixed.cc | 2 src/stanExports_HDIdUnif.cc | 2 src/stanExports_HDIdUnifFixed.cc | 2 src/stanExports_HDIstandard.cc | 2 src/stanExports_HDIstandardFixed.cc | 2 src/stanExports_HDIstandardHetero.cc | 2 22 files changed, 157 insertions(+), 135 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.3.1 dated 2022-08-08 and 1.3.2 dated 2022-09-12
DESCRIPTION | 8 +- MD5 | 12 +-- NEWS.md | 10 +++ R/jsBasicGadget.R | 10 +++ R/roc.R | 57 ++++++++++++++++-- R/timeroc.R | 148 ++++++++++++++++++++++++++++++++++++++++++++++++- inst/doc/jsmodule.html | 4 - 7 files changed, 227 insertions(+), 22 deletions(-)
Title: A Logging Utility Focus on Clinical Trial Programming Workflows
Description: A utility to facilitate the logging and review of R programs in clinical trial programming workflows.
Author: Nathan Kosiba [aut, cre] ,
Thomas Bermudez [aut],
Ben Straub [aut],
Michael Rimler [aut],
Nicholas Masel [aut],
GSK/Atorus JPT [cph, fnd]
Maintainer: Nathan Kosiba <Nathan.Kosiba@atorusresearch.com>
Diff between logrx versions 0.1.0 dated 2022-06-17 and 0.1.1 dated 2022-09-12
DESCRIPTION | 11 ++++++----- MD5 | 24 +++++++++++++----------- NEWS.md | 4 ++++ R/interact.R | 12 ++++++++---- README.md | 11 ++++++++--- build/vignette.rds |binary inst/doc/logrx.Rmd | 4 ++-- inst/doc/logrx.html | 4 ++-- inst/rstudio/addins.dcf | 3 ++- man/figures/logo.png |binary man/set_log_name_path.Rd | 13 ++++--------- tests/testthat/ref/ex1.log |only tests/testthat/ref/safely_loudly_test_file.log |only vignettes/logrx.Rmd | 4 ++-- 14 files changed, 51 insertions(+), 39 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-11 0.7.12
2022-06-21 0.7.11
2022-05-28 0.7.10
2022-01-20 0.7.9
2022-01-12 0.7.8
Title: Multivariate Data Handling with S4 Classes and Sparse Matrices
Description: An S4 update of the 'mefa' package
using sparse matrices for enhanced efficiency.
Sparse array-like objects are supported via
lists of sparse matrices.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between mefa4 versions 0.3-8 dated 2021-10-06 and 0.3-9 dated 2022-09-12
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/00mefa4classes.R | 3 ++- R/00mefa4methods.R | 3 ++- R/Mefa.R | 3 ++- R/Melt.R | 12 ++++++++---- R/Xtab.R | 7 ++++--- R/mbind2.R | 3 ++- R/zzz.R | 5 +++++ build/partial.rdb |binary 10 files changed, 39 insertions(+), 25 deletions(-)
Title: General Linear Mixed Models for Gene-Level Differential
Expression
Description: Using mixed effects models to analyse longitudinal gene expression can highlight differences between sample groups over time. The most widely used differential gene expression tools are unable to fit linear mixed effect models, and are less optimal for analysing longitudinal data. This package provides negative binomial and Gaussian mixed effects models to fit gene expression and other biological data across repeated samples. This is particularly useful for investigating changes in RNA-Sequencing gene expression between groups of individuals over time, as described in: Rivellese, F., Surace, A. E., Goldmann, K., Sciacca, E., Cubuk, C., Giorli, G., ... Lewis, M. J., & Pitzalis, C. (2022) Nature medicine <doi:10.1038/s41591-022-01789-0>.
Author: Myles Lewis [aut, cre] ,
Katriona Goldmann [aut] ,
Elisabetta Sciacca [aut] ,
Cankut Cubuk [ctb] ,
Anna Surace [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between glmmSeq versions 0.4.0 dated 2022-08-12 and 0.5.1 dated 2022-09-12
DESCRIPTION | 22 +- MD5 | 41 ++--- NAMESPACE | 4 NEWS.md | 21 +- R/fcPlot.R | 63 +++---- R/ggmodelPlot.R | 52 +++--- R/glmmRefit.R | 25 +-- R/glmmSeq.R | 323 +++++++++++++++++++++++++---------------- R/lmer_wald.R | 32 +++- R/lmmSeq.R | 40 +---- R/maPlot.R | 10 - R/modelPlot.R | 11 + R/summary_lmmSeq.R | 8 - inst/doc/glmmSeq.R | 50 ++---- inst/doc/glmmSeq.html | 318 +++++++++++++++++++++++++++++++--------- inst/doc/glmmSeq.rmd | 160 +++++++++++--------- man/ggmodelPlot.Rd | 4 man/glmmRefit.Rd | 4 man/glmmSeq.Rd | 34 +++- man/modelPlot.Rd | 4 vignettes/glmmSeq.rmd | 160 +++++++++++--------- vignettes/r4ra_glmm_fcplot.png |only 22 files changed, 868 insertions(+), 518 deletions(-)
Title: Fast Functions for Prime Numbers
Description: Fast functions for dealing with prime numbers, such as testing
whether a number is prime and generating a sequence prime numbers.
Additional functions include finding prime factors and Ruth-Aaron pairs,
finding next and previous prime numbers in the series, finding or estimating
the nth prime, estimating the number of primes less than or equal to an
arbitrary number, computing primorials, prime k-tuples (e.g., twin primes),
finding the greatest common divisor and smallest (least) common multiple,
testing whether two numbers are coprime, and computing Euler's totient
function. Most functions are vectorized for speed and convenience.
Author: Os Keyes [aut, cre],
Paul Egeler [aut]
Maintainer: Os Keyes <ironholds@gmail.com>
Diff between primes versions 1.1.0 dated 2020-09-03 and 1.4.0 dated 2022-09-12
primes-1.1.0/primes/man/phi.Rd |only primes-1.1.0/primes/man/prime_factors.Rd |only primes-1.1.0/primes/man/ruth_aaron_pairs.Rd |only primes-1.4.0/primes/DESCRIPTION | 10 +- primes-1.4.0/primes/MD5 | 38 +++---- primes-1.4.0/primes/NAMESPACE | 5 - primes-1.4.0/primes/R/RcppExports.R | 77 +++------------- primes-1.4.0/primes/R/gcd.R |only primes-1.4.0/primes/R/k_tuple.R | 9 - primes-1.4.0/primes/R/phi.R | 18 +-- primes-1.4.0/primes/R/ruth_aaron_pairs.R | 28 ++--- primes-1.4.0/primes/man/gcd.Rd | 35 ++++++- primes-1.4.0/primes/man/k_tuple.Rd | 9 + primes-1.4.0/primes/src/RcppExports.cpp | 67 +++++++++++-- primes-1.4.0/primes/src/gcd.cpp | 53 +++++------ primes-1.4.0/primes/src/k_tuple.cpp | 57 +++++++++-- primes-1.4.0/primes/src/prime_factors.cpp | 50 ++++------ primes-1.4.0/primes/src/primes.h | 6 + primes-1.4.0/primes/tests/testthat/test_gcd.R | 10 ++ primes-1.4.0/primes/tests/testthat/test_k_tuple.R | 35 +++++++ primes-1.4.0/primes/tests/testthat/test_phi.R | 12 +- primes-1.4.0/primes/tests/testthat/test_prime_factors.R | 44 ++++----- 22 files changed, 335 insertions(+), 228 deletions(-)
Title: A Framework for Building HTTP API
Description: Allows to easily create high-performance full featured HTTP APIs from R
functions. Provides high-level classes such as 'Request', 'Response',
'Application', 'Middleware' in order to streamline server side
application development. Out of the box allows to serve requests using
'Rserve' package, but flexible enough to integrate with other HTTP servers
such as 'httpuv'.
Author: Dmitry Selivanov [aut, cre] ,
Artem Klevtsov [aut] ,
David Zimmermann [ctb],
rexy.ai [cph, fnd]
Maintainer: Dmitry Selivanov <ds@rexy.ai>
Diff between RestRserve versions 1.2.0 dated 2022-06-09 and 1.2.1 dated 2022-09-12
DESCRIPTION | 8 - MD5 | 64 ++++----- NEWS.md | 118 +++++++++--------- R/CORSMiddleware.R | 1 R/ETagMiddleware.R | 1 R/logging.R | 1 README.md | 4 inst/doc/Authentication.html | 253 ++++++++++++++++++++++++++++++++++++-- inst/doc/ContentHandlers.html | 275 ++++++++++++++++++++++++++++++++++++++---- inst/doc/Logging.html | 262 ++++++++++++++++++++++++++++++++++++---- inst/doc/Middleware.html | 266 +++++++++++++++++++++++++++++++++++++--- inst/doc/RestRserve.Rmd | 2 inst/doc/RestRserve.html | 257 ++++++++++++++++++++++++++++++++++++--- man/Application.Rd | 66 +++++----- man/ApplicationProcess.Rd | 18 +- man/AuthBackend.Rd | 18 +- man/AuthBackendBasic.Rd | 24 +-- man/AuthBackendBearer.Rd | 24 +-- man/AuthMiddleware.Rd | 18 -- man/Backend.Rd | 18 +- man/BackendRserve.Rd | 36 ++--- man/CORSMiddleware.Rd | 18 -- man/ContentHandlers.Rd | 48 +++---- man/ETagMiddleware.Rd | 44 +++--- man/EncodeDecodeMiddleware.Rd | 18 -- man/HTTPError.Rd | 218 ++++++++++++++++----------------- man/Logger.Rd | 66 +++++----- man/Middleware.Rd | 12 - man/Request.Rd | 60 ++++----- man/Response.Rd | 102 +++++++-------- man/RestRserve-package.Rd | 44 ++++-- man/Router.Rd | 30 ++-- vignettes/RestRserve.Rmd | 2 33 files changed, 1752 insertions(+), 644 deletions(-)
Title: Isoscape Computation and Inference of Spatial Origins using
Mixed Models
Description: Building isoscapes using mixed models and inferring the geographic
origin of samples based on their isotopic ratios. This package is essentially a
simplified interface to several other packages which implements a new
statistical framework based on mixed models. It uses 'spaMM' for fitting and
predicting isoscapes, and assigning an organism's origin depending on its
isotopic ratio. 'IsoriX' also relies heavily on the package 'rasterVis' for
plotting the maps produced with 'raster' using 'lattice'.
Author: Alexandre Courtiol [aut, cre] ,
Francois Rousset [aut] ,
Marie-Sophie Rohwaeder [aut],
Stephanie Kramer-Schadt [aut]
Maintainer: Alexandre Courtiol <alexandre.courtiol@gmail.com>
Diff between IsoriX versions 0.8.2 dated 2020-09-16 and 0.8.3 dated 2022-09-12
IsoriX-0.8.2/IsoriX/R/isosim.R |only IsoriX-0.8.2/IsoriX/man/isosim.Rd |only IsoriX-0.8.3/IsoriX/DESCRIPTION | 17 IsoriX-0.8.3/IsoriX/MD5 | 101 +- IsoriX-0.8.3/IsoriX/NAMESPACE | 3 IsoriX-0.8.3/IsoriX/R/IsoriX-dataset.R | 232 ++--- IsoriX-0.8.3/IsoriX/R/IsoriX-package.R | 53 - IsoriX-0.8.3/IsoriX/R/calibfit.R | 915 +++++++++++++++----- IsoriX-0.8.3/IsoriX/R/create_aliens.R | 56 - IsoriX-0.8.3/IsoriX/R/getelev.R | 222 +++- IsoriX-0.8.3/IsoriX/R/isofind.R | 165 ++- IsoriX-0.8.3/IsoriX/R/isofit.R | 221 ++-- IsoriX-0.8.3/IsoriX/R/isoscape.R | 125 +- IsoriX-0.8.3/IsoriX/R/options.R | 6 IsoriX-0.8.3/IsoriX/R/plots.R | 409 +++++--- IsoriX-0.8.3/IsoriX/R/prepcipitate.R | 51 - IsoriX-0.8.3/IsoriX/R/prepraster.R | 104 +- IsoriX-0.8.3/IsoriX/R/prepsources.R | 129 +- IsoriX-0.8.3/IsoriX/R/zzz.R | 104 +- IsoriX-0.8.3/IsoriX/data/ElevRasterDE.rda |binary IsoriX-0.8.3/IsoriX/data/PrecipBrickDE.rda |binary IsoriX-0.8.3/IsoriX/inst/NEWS.Rd | 43 IsoriX-0.8.3/IsoriX/man/AssignDataAlien.Rd | 10 IsoriX-0.8.3/IsoriX/man/AssignDataBat.Rd | 14 IsoriX-0.8.3/IsoriX/man/AssignDataBat2.Rd | 12 IsoriX-0.8.3/IsoriX/man/CalibDataAlien.Rd | 22 IsoriX-0.8.3/IsoriX/man/CalibDataBat.Rd | 34 IsoriX-0.8.3/IsoriX/man/CalibDataBat2.Rd | 41 IsoriX-0.8.3/IsoriX/man/CountryBorders.Rd | 8 IsoriX-0.8.3/IsoriX/man/ElevRasterDE.Rd | 10 IsoriX-0.8.3/IsoriX/man/GNIPDataDE.Rd | 24 IsoriX-0.8.3/IsoriX/man/GNIPDataEUagg.Rd | 24 IsoriX-0.8.3/IsoriX/man/IsoriX-package.Rd | 53 - IsoriX-0.8.3/IsoriX/man/OceanMask.Rd | 8 IsoriX-0.8.3/IsoriX/man/PrecipBrickDE.Rd | 6 IsoriX-0.8.3/IsoriX/man/calibfit.Rd | 409 +++++++- IsoriX-0.8.3/IsoriX/man/create_aliens.Rd | 36 IsoriX-0.8.3/IsoriX/man/downloadfile.Rd | 14 IsoriX-0.8.3/IsoriX/man/getelev.Rd | 101 +- IsoriX-0.8.3/IsoriX/man/getprecip.Rd | 24 IsoriX-0.8.3/IsoriX/man/isofind.Rd | 82 + IsoriX-0.8.3/IsoriX/man/isofit.Rd | 175 +-- IsoriX-0.8.3/IsoriX/man/isomultifit.Rd | 34 IsoriX-0.8.3/IsoriX/man/isomultiscape.Rd | 30 IsoriX-0.8.3/IsoriX/man/isopalette2.Rd | 17 IsoriX-0.8.3/IsoriX/man/isoscape.Rd | 30 IsoriX-0.8.3/IsoriX/man/options.Rd | 4 IsoriX-0.8.3/IsoriX/man/plots.Rd | 233 ++--- IsoriX-0.8.3/IsoriX/man/prepcipitate.Rd | 34 IsoriX-0.8.3/IsoriX/man/prepraster.Rd | 69 - IsoriX-0.8.3/IsoriX/man/prepsources.Rd | 74 - IsoriX-0.8.3/IsoriX/tests/testthat/test_internals.R | 2 IsoriX-0.8.3/IsoriX/tests/testthat/test_tibbles.R |only 53 files changed, 2936 insertions(+), 1654 deletions(-)
More information about BoundEdgeworth at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-31 0.5.1
2022-07-08 0.5.0
2022-05-30 0.4.0
Title: Handling Taxonomic Lists
Description: Handling taxonomic lists through objects of class 'taxlist'.
This package provides functions to import species lists from 'Turboveg'
(<https://www.synbiosys.alterra.nl/turboveg/>) and the possibility to create
backups from resulting R-objects.
Also quick displays are implemented as summary-methods.
Author: Miguel Alvarez [aut, cre] ,
Zachary Foster [ctb] ,
Sam Levin [rev],
Margaret Siple [rev]
Maintainer: Miguel Alvarez <kamapu78@gmail.com>
Diff between taxlist versions 0.2.2 dated 2021-07-15 and 0.2.3 dated 2022-09-12
taxlist-0.2.2/taxlist/R/as.list.R |only taxlist-0.2.2/taxlist/man/as.list.Rd |only taxlist-0.2.2/taxlist/man/figures/taxlist_logo.png |only taxlist-0.2.2/taxlist/tests |only taxlist-0.2.3/taxlist/DESCRIPTION | 16 taxlist-0.2.3/taxlist/MD5 | 166 ++--- taxlist-0.2.3/taxlist/NAMESPACE | 16 taxlist-0.2.3/taxlist/NEWS.md | 22 taxlist-0.2.3/taxlist/R/Easplist-data.R | 50 - taxlist-0.2.3/taxlist/R/Extract.R | 166 ++--- taxlist-0.2.3/taxlist/R/accepted_name.R | 602 +++++++++++--------- taxlist-0.2.3/taxlist/R/as.R |only taxlist-0.2.3/taxlist/R/backup_object.R | 244 ++++---- taxlist-0.2.3/taxlist/R/clean.R | 217 +++---- taxlist-0.2.3/taxlist/R/clean_strings.R | 148 ++-- taxlist-0.2.3/taxlist/R/count_taxa.R | 305 +++++----- taxlist-0.2.3/taxlist/R/deprecated-functions.R | 168 +++-- taxlist-0.2.3/taxlist/R/df2taxlist.R | 394 +++++++------ taxlist-0.2.3/taxlist/R/dissect_name.R | 96 +-- taxlist-0.2.3/taxlist/R/get_children.R | 272 ++++----- taxlist-0.2.3/taxlist/R/imports.R | 6 taxlist-0.2.3/taxlist/R/indented_list.R | 253 +++++--- taxlist-0.2.3/taxlist/R/internal.R | 229 +++---- taxlist-0.2.3/taxlist/R/levels.R | 170 +++-- taxlist-0.2.3/taxlist/R/match_names.R | 378 +++++++----- taxlist-0.2.3/taxlist/R/merge_taxa.R | 316 +++++----- taxlist-0.2.3/taxlist/R/print_name.R | 406 ++++++++----- taxlist-0.2.3/taxlist/R/replace_x.R | 272 ++++----- taxlist-0.2.3/taxlist/R/subset.R | 150 ++-- taxlist-0.2.3/taxlist/R/summary.R | 542 ++++++++++-------- taxlist-0.2.3/taxlist/R/tax2traits.R | 228 ++++--- taxlist-0.2.3/taxlist/R/taxlist-class.R | 464 ++++++++------- taxlist-0.2.3/taxlist/R/taxlist-package.R | 72 +- taxlist-0.2.3/taxlist/R/taxon_names.R | 451 ++++++++------- taxlist-0.2.3/taxlist/R/taxon_relations.R | 631 +++++++++++---------- taxlist-0.2.3/taxlist/R/taxon_traits.R | 286 +++++---- taxlist-0.2.3/taxlist/R/taxon_views.R | 271 ++++----- taxlist-0.2.3/taxlist/R/tnrs.R | 199 +++--- taxlist-0.2.3/taxlist/R/tv2taxlist.R | 112 +-- taxlist-0.2.3/taxlist/build/partial.rdb |binary taxlist-0.2.3/taxlist/build/vignette.rds |binary taxlist-0.2.3/taxlist/data/Easplist.rda |binary taxlist-0.2.3/taxlist/inst/doc/taxlist-intro.R | 2 taxlist-0.2.3/taxlist/inst/doc/taxlist-intro.Rmd | 2 taxlist-0.2.3/taxlist/inst/doc/taxlist-intro.html | 416 +++++++++++-- taxlist-0.2.3/taxlist/man/Easplist-data.Rd | 4 taxlist-0.2.3/taxlist/man/Extract.Rd | 3 taxlist-0.2.3/taxlist/man/accepted_name.Rd | 7 taxlist-0.2.3/taxlist/man/backup_object.Rd | 11 taxlist-0.2.3/taxlist/man/clean.Rd | 3 taxlist-0.2.3/taxlist/man/clean_strings.Rd | 2 taxlist-0.2.3/taxlist/man/coerce-methods.Rd |only taxlist-0.2.3/taxlist/man/count_taxa.Rd | 5 taxlist-0.2.3/taxlist/man/df2taxlist.Rd | 95 +-- taxlist-0.2.3/taxlist/man/dissect_name.Rd | 7 taxlist-0.2.3/taxlist/man/figures/logo.png |only taxlist-0.2.3/taxlist/man/get_children.Rd | 9 taxlist-0.2.3/taxlist/man/indented_list.Rd | 7 taxlist-0.2.3/taxlist/man/levels.Rd | 7 taxlist-0.2.3/taxlist/man/match_names.Rd | 16 taxlist-0.2.3/taxlist/man/merge_taxa.Rd | 9 taxlist-0.2.3/taxlist/man/print_name.Rd | 86 +- taxlist-0.2.3/taxlist/man/replace_x.Rd | 41 - taxlist-0.2.3/taxlist/man/subset.Rd | 9 taxlist-0.2.3/taxlist/man/summary.Rd | 13 taxlist-0.2.3/taxlist/man/tax2traits.Rd | 9 taxlist-0.2.3/taxlist/man/taxlist-class.Rd | 1 taxlist-0.2.3/taxlist/man/taxon_names.Rd | 15 taxlist-0.2.3/taxlist/man/taxon_relations.Rd | 27 taxlist-0.2.3/taxlist/man/taxon_traits.Rd | 11 taxlist-0.2.3/taxlist/man/taxon_views.Rd | 9 taxlist-0.2.3/taxlist/man/tv2taxlist.Rd | 44 - taxlist-0.2.3/taxlist/vignettes/taxlist-intro.Rmd | 2 73 files changed, 5193 insertions(+), 3997 deletions(-)
Title: Simultaneous Non-Gaussian Component Analysis
Description: Implementation of SING algorithm to extract joint and individual non-Gaussian components from two datasets. SING uses an objective function that maximizes the skewness and kurtosis of latent components with a penalty to enhance the similarity between subject scores. Unlike other existing methods, SING does not use PCA for dimension reduction, but rather uses non-Gaussianity, which can improve feature extraction. Benjamin B.Risk, Irina Gaynanova (2021) <doi:10.1214/21-AOAS1466>.
Author: Liangkang Wang [aut, cre] ,
Irina Gaynanova [aut] ,
Benjamin Risk [aut]
Maintainer: Liangkang Wang <wangliangkang1130@gmail.com>
Diff between singR versions 0.1.0 dated 2022-08-22 and 0.1.1 dated 2022-09-12
DESCRIPTION | 8 MD5 | 40 +-- NAMESPACE | 6 R/Basic_functions.r | 51 +++- R/Match&Permutation_Functions.R | 113 +++++++++ R/UpdateFunctions.R | 4 R/jngcaFunctions.R | 120 --------- R/lngca.R | 2 R/singR.R | 3 inst/doc/singR-tutorial.R | 17 + inst/doc/singR-tutorial.Rmd | 150 ++---------- inst/doc/singR-tutorial.html | 488 +++++++++++++--------------------------- man/aveM.Rd | 22 + man/calculateJB.Rd | 5 man/curvilinear.Rd | 2 man/curvilinear_c.Rd | 2 man/lngca.Rd | 2 man/pmse.Rd | 16 + man/singR.Rd | 3 man/theta2W.Rd | 4 vignettes/singR-tutorial.Rmd | 150 ++---------- 21 files changed, 469 insertions(+), 739 deletions(-)
Title: Regularized Greedy Forest
Description: Regularized Greedy Forest wrapper of the 'Regularized Greedy Forest' <https://github.com/RGF-team/rgf/tree/master/python-package> 'python' package, which also includes a Multi-core implementation (FastRGF) <https://github.com/RGF-team/rgf/tree/master/FastRGF>.
Author: Lampros Mouselimis [aut, cre] ,
Ryosuke Fukatani [cph] ,
Nikita Titov [cph] ,
Tong Zhang [cph] ,
Rie Johnson [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between RGF versions 1.1.0 dated 2022-09-05 and 1.1.1 dated 2022-09-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ README.md | 3 --- inst/doc/the_RGF_package.html | 4 ++-- tests/testthat/test-RGF_package.R | 28 +++++++++++++++++++++++----- 6 files changed, 38 insertions(+), 19 deletions(-)
Title: Simulate Expression Data from 'igraph' Networks
Description: Functions to develop simulated continuous data (e.g., gene expression) from a sigma covariance matrix derived from a graph structure in 'igraph' objects. Intended to extend 'mvtnorm' to take 'igraph' structures rather than sigma matrices as input. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. Here we present a versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from a multivariate normal distribution derived from a graph structure. This package allows the simulation of biological pathways from a graph structure based on a statistical model of gene expression. For example methods to infer biological pathways and gene regulatory networks from gene expression data can be tested on simulated datasets using this framework. This also allows for pathway structures to [...truncated...]
Author: S. Thomas Kelly [aut, cre],
Michael A. Black [aut, ths],
Robrecht Cannoodt [ctb],
Jason Cory Brunson [ctb]
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>
Diff between graphsim versions 1.0.2 dated 2021-07-30 and 1.0.3 dated 2022-09-12
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 2 -- NEWS.md | 10 ++++++++++ R/graphsim-package.R | 2 +- R/laplacian.R | 2 -- README.md | 10 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 +- inst/doc/simulate_expression.html | 2 +- man/graphsim-package.Rd | 2 +- vignettes/simulate_expression.Rmd | 2 +- 13 files changed, 38 insertions(+), 32 deletions(-)